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L

Likelihood - package Likelihood
Provides classes for calculating the likelihood of a tree given a model and an alignment.
Likelihood - Class in Likelihood
Represents the simplest possible likelihood result, i.e.
Likelihood(double, Parameters) - Constructor for class Likelihood.Likelihood
Creates a simple likelihood result
likelihood(Alignment) - Method in interface ModelTest.Adapter
Return the likelihood of the adapter given the distinct alignment
likelihood(Alignment) - Method in class ModelTest.EmpiricalAdapter
 
likelihood(Alignment) - Method in class ModelTest.EqualAdapter
 
likelihood(Alignment) - Method in class ModelTest.IdentityAdapter
 
limitToTaxa(Collection<String>) - Method in class Alignments.Alignment
Returns a new Alignment which is the same as this one except it is limited to certain taxa
limitToTaxa(Collection<String>) - Method in class Alignments.Site
Returns a new Site which is the same as this one except it is limited to certain taxa
ln() - Method in interface Maths.Real
Returns the natural logarithm of this Real
ln() - Method in class Maths.SmallDouble
 
ln() - Method in class Maths.StandardDouble
 
ln1m() - Method in interface Maths.Real
Returns the natural logithm of one minus the value of this Real
ln1m() - Method in class Maths.SmallDouble
 
ln1m() - Method in class Maths.StandardDouble
 
lower() - Method in class Utils.Range
Gets the lower value
LUDecomposition - Class in Maths
LU Decomposition.
LUDecomposition(SquareMatrix) - Constructor for class Maths.LUDecomposition
LU Decomposition
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